Sorry, the protein region has no volume? This means that the solvent
content is 0 or 1. Try a value in between.
Sorry, this is an invalid access code You need to check out your
solve2.access file. If SOLVE runs, so should RESOLVE.
Segmentation fault (core dump, program never starts) There can be several
causes. On linux and SGI this can happen if your system does not match
the system the binaries were compiled on. Solution: email
terwilliger@lanl.gov and I'll send
you instructions on how to compile on your own machine.
Also on
an SGI: This can happen if your machine doesn't have enough memory allocated
to you. To get around this (at least on an SGI), use the command: "unlimit"
. You can put this as one line in your .cshrc file if you use csh. The
same works on an Alpha too. You may also need to increase your swap space
in some cases.
Segmentation fault (core dump after "Writing peaks to.."), same fix
as above: use the command: "unlimit"; may need to increase your swap space
or use "small" version.
killed This happens if you run the too big a version of RESOLVE on an
SGI or if you're already running a big job. See the above command "unlimit"
to fix it or use a smaller version.
/sbin/loader: Fatal Error: Program datasize exceeds process datasize
limit. This is an error message you get with an Alpha when you don't have
enough memory allocated to yourself. To get around this, edit your ".cshrc"
or similar file to include the line "unlimit" or use the "small" version.
Sorry, nothing in bins of density? The electron density map you input
probably has no reflections in the resolution range or is all zeros.
Sorry, cannot add any more onto the "LABIN" line (max 132 characters).
RESOLVE cannot use more than 132 characters in a labin line. Sorry!
Sorry: uninterpretable value or keyword. RESOLVE could not parse the
input. It stops when this happens. Usually a keyword it does not recognize
was input. Note that RESOLVE does not recognize partial keywords, you have
to type the whole word in.
Sorry, need to make n_map_max at least [some number]. The version of
RESOLVE you have is not big enough for your dataset. Try the "giant" (resolve_giant)
or even the "huge" (resolve_huge) version. If that does not work, contact
the author for a bigger version.
sorry, this map has no density. The electron density map you input probably
has no reflections in the resolution range or is all zeros.
Sorry, need to increase n_refl_max The version of RESOLVE you have is
not big enough for your dataset. Try the giant or huge versions (resolve_giant
or resolve_huge). If that does not work, contact the author for a bigger
version.
rms of this map is nan avg = nan This can happen if there are "NaN"
(empty) entries in your mtz file. This version of RESOLVE does not always
handle these correctly. If you remove them (mtzdump, remove lines with
question marks, f2mtz) it should be ok.
resolve: Open failed: File: SYMOP. RESOLVE needs the CCP4 symmetry data
file "symop.lib". Usually this is located in /usr/local/lib/solve after
you download resolve. If it is not there, then you'll need to find out
where it is, then define the environmental variable SYMOP. Similarly,
SYMINFO needs to be defined.
Sorry, cannot read segment library needed for automatic model-building.
Or Sorry, cannot properly read fragment libraries .. RESOLVE model-building
uses a library of helix/strand segments and a library of fragments. These
are normally located in /usr/local/lib/solve/segments/ after standard installation
of SOLVE/RESOLVE. If you define $SOLVEDIR then RESOLVE will expect to find
these libraries in $SOLVEDIR/segments.
Can RESOLVE...
Extend phases or fill in missing reflections? Yes, any reflections
with non-zero F in your input file that are in your resolution limits are
filled in by RESOLVE (version 1.04 or higher). Additionally with
version 2.01 or higher, all reflections that are completely missing are
filled in as well if you specify "fill"
Use NC-symmetry? Yes, starting with version 2.0.
Phase from a partial model? Yes, use iterative model-building
for this one
Use a MR starting model? Yes, use prime-and-switch phasing
or use iterative model rebuilding
Use a mask that I input? Yes, sort of. Make a model that covers
the region you want masked. Read the model in with model mask_model.pdb.
Then specify use_model_mask and that will be used. You can set the
radius around each atom to be masked with rad_mask xxx